t1 <- Sys.time()

sampd <- list.dirs("/media/knausb/E737-9B48/releases/scaffolded/")
sampd <- grep("scaffolded/$", sampd, value = TRUE, invert = TRUE)
sampd <- grep("EDTAOutput", sampd, value = TRUE, invert = TRUE)

#sampd <- sampd[ c(2:5, grep("EH23", sampd)) ]
#sampd <- sampd[2:5]

#sub(".+//", "", sampd)
sampn <- unlist(lapply(strsplit(sampd, split = "//"), function(x){x[2]}))

Queries

my_queries <- data.frame( 
  query = c("45S", "26S", "5.8S", "18S", "5S", 
            "CS-237_satelite", "CsatSD_centromere_237bp", "CsatSD_subtelomere_370bp"),
  Length = c(9382, 1544, 157, 1552, 259, 557, 237, 370 )
  )
knitr::kable(my_queries)
query Length
45S 9382
26S 1544
5.8S 157
18S 1552
5S 259
CS-237_satelite 557
CsatSD_centromere_237bp 237
CsatSD_subtelomere_370bp 370

nuccomp

fast_win

Ideo function

source("Rfunctions.R")
t4 <- Sys.time()

sampd <- list.dirs("/media/knausb/E737-9B48/releases/scaffolded/")
sampd <- grep("scaffolded/$", sampd, value = TRUE, invert = TRUE)
sampd <- grep("EDTAOutput", sampd, value = TRUE, invert = TRUE)

#sampd <- sampd[ c(2:5, grep("EH23", sampd)) ]
#sampd <- sampd[ c(2:11, grep("EH23", sampd)) ]

#sampd <- sampd[ c(1:2, grep("EH23", sampd)) ]
#sampd <- sampd[ c(1:10, grep("EH23", sampd)) ]

#sampd <- sampd[ c(1:16, grep("EH23", sampd)) ]
#sampd <- sampd[ c(1:22, grep("EH23", sampd)) ]
#sampd <- sampd[ 1:30 ]
#sampd <- sampd[2:5]

#undebug(plot_ideo)
# p1 <- plot_ideo( sampd[1] )
# p1 <- plot_ideo( sampd[5] )
# p1 <- plot_ideo( sampd[6] )
# p1

# plist[[1]] <- plot_ideo( sampd[1] )
# plist[[2]] <- plot_ideo( sampd[2] )
# 
# plist[[1]]
# plist[[2]]


plist <- vector( mode = "list", length = length(sampd) )
for( i in 1:length(sampd) ){
  message("Processing sample ", i, " of ", length(sampd), ".")
  plist[[i]] <- plot_ideo( sampd[i] )
}

# plist[[1]]

#sub(".+//", "", sampd)
#sampn <- unlist(lapply(strsplit(sampd, split = "//"), function(x){x[2]}))
library(ggpubr)

my_ps <- 1:4
#ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))


for(i in 1:ceiling(length(plist)/4) ){
  my_ps <- 1:4
  my_ps <- my_ps + (i - 1) * 4
  if( my_ps[length(my_ps)] > length(plist) ){
    my_ps <- my_ps[1]:length(plist)
  }
  print(ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 2,
                   labels = c("A", "B", "C", "D")))
}
**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

**Figure X.** Ideogram of the *Cannabis sativa* genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the 'CpG' motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome.

Figure X. Ideogram of the Cannabis sativa genome. Each chromosome is presented as a set of 1 Mbp windows where the width is proportional to the abundance of the ‘CpG’ motif (wide is low abundance, narrow is high abundance) and colored by gene density (cool or blue colors are low gene density and hot or yellow colors are high gene density). The 45S, 26S, 18S, and 5.8S probes are in firebrick red, the 5S probes are in black, Cannabinoids (CBCAS, CBDAS, THCAS, OAC) are in forest green, the centromeric and telomeric probes are in Dodger blue and are offset from the center of each chromosome. 

# for(i in 1:(length(plist)/6) ){
#   my_ps <- 1:6
#   my_ps <- my_ps + (i - 1) * 6
#   if( my_ps[length(my_ps)] > length(plist) ){
#     my_ps <- my_ps[1]:length(plist)
#   }
#   print(ggarrange( plotlist = plist[my_ps], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F")))
# }



#ggarrange( plotlist = plist[1:6], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))
#ggarrange( plotlist = plist[7:12], ncol = 2, nrow = 3, labels = c("A", "B", "C", "D", "E", "F"))
t99 <- Sys.time()
t99 - t1
## Time difference of 4.692166 mins